[BioC] error with accessing biomaRt attributes

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Sep 16 16:45:27 CEST 2009


On Sep 16, 2009, at 3:47 AM, Kishor Tappita wrote:

> Dear List,
> I get the below error while trying to access biomaRt attributes.
>> getBM(attributes = c("entrezgene"),values = c 
>> ("202763_at","209310_s_at"),mart =ensembl)
> Error in getBM(attributes = c("entrezgene"), values = c("202763_at",
> "209310_s_at"),  :
> The query to the BioMart webservice returned an invalid result:
> biomaRt expected a character string of length 1. Please report this to
> the mailing list.

Aren't you forgetting to pass in the "filters" parameter to the getBM  

It looks like you're trying to get an entrezgene id from some affy  
probe id? You have to tell the function what types of "things" you're  
passing into "values" using the "filter" param.

Look closely (again) at the code in the Example section of ?getBM


Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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